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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 13-49522084-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=49522084&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 49522084,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000378319.8",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "c.547C>A",
"hgvs_p": "p.Pro183Thr",
"transcript": "NM_001040443.3",
"protein_id": "NP_001035533.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 331,
"cds_start": 547,
"cds_end": null,
"cds_length": 996,
"cdna_start": 596,
"cdna_end": null,
"cdna_length": 1356,
"mane_select": "ENST00000378319.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "c.547C>A",
"hgvs_p": "p.Pro183Thr",
"transcript": "ENST00000378319.8",
"protein_id": "ENSP00000367570.3",
"transcript_support_level": 1,
"aa_start": 183,
"aa_end": null,
"aa_length": 331,
"cds_start": 547,
"cds_end": null,
"cds_length": 996,
"cdna_start": 596,
"cdna_end": null,
"cdna_length": 1356,
"mane_select": "NM_001040443.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "c.430C>A",
"hgvs_p": "p.Pro144Thr",
"transcript": "ENST00000488958.5",
"protein_id": "ENSP00000417539.1",
"transcript_support_level": 1,
"aa_start": 144,
"aa_end": null,
"aa_length": 292,
"cds_start": 430,
"cds_end": null,
"cds_length": 879,
"cdna_start": 558,
"cdna_end": null,
"cdna_length": 1318,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "n.430C>A",
"hgvs_p": null,
"transcript": "ENST00000465045.5",
"protein_id": "ENSP00000418630.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1626,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETDB2-PHF11",
"gene_hgnc_id": null,
"hgvs_c": "c.2029C>A",
"hgvs_p": "p.Pro677Thr",
"transcript": "NM_001320727.2",
"protein_id": "NP_001307656.1",
"transcript_support_level": null,
"aa_start": 677,
"aa_end": null,
"aa_length": 825,
"cds_start": 2029,
"cds_end": null,
"cds_length": 2478,
"cdna_start": 2954,
"cdna_end": null,
"cdna_length": 3714,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "c.430C>A",
"hgvs_p": "p.Pro144Thr",
"transcript": "NM_001040444.3",
"protein_id": "NP_001035534.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 292,
"cds_start": 430,
"cds_end": null,
"cds_length": 879,
"cdna_start": 758,
"cdna_end": null,
"cdna_length": 1518,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "c.430C>A",
"hgvs_p": "p.Pro144Thr",
"transcript": "NM_001419873.1",
"protein_id": "NP_001406802.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 292,
"cds_start": 430,
"cds_end": null,
"cds_length": 879,
"cdna_start": 1111,
"cdna_end": null,
"cdna_length": 1871,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "c.430C>A",
"hgvs_p": "p.Pro144Thr",
"transcript": "NM_001419874.1",
"protein_id": "NP_001406803.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 292,
"cds_start": 430,
"cds_end": null,
"cds_length": 879,
"cdna_start": 1145,
"cdna_end": null,
"cdna_length": 1905,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "c.430C>A",
"hgvs_p": "p.Pro144Thr",
"transcript": "NM_001419875.1",
"protein_id": "NP_001406804.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 292,
"cds_start": 430,
"cds_end": null,
"cds_length": 879,
"cdna_start": 949,
"cdna_end": null,
"cdna_length": 1709,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "c.430C>A",
"hgvs_p": "p.Pro144Thr",
"transcript": "NM_001419876.1",
"protein_id": "NP_001406805.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 292,
"cds_start": 430,
"cds_end": null,
"cds_length": 879,
"cdna_start": 983,
"cdna_end": null,
"cdna_length": 1743,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "c.430C>A",
"hgvs_p": "p.Pro144Thr",
"transcript": "ENST00000357596.7",
"protein_id": "ENSP00000350209.3",
"transcript_support_level": 5,
"aa_start": 144,
"aa_end": null,
"aa_length": 292,
"cds_start": 430,
"cds_end": null,
"cds_length": 879,
"cdna_start": 706,
"cdna_end": null,
"cdna_length": 1471,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "c.409C>A",
"hgvs_p": "p.Pro137Thr",
"transcript": "ENST00000426879.5",
"protein_id": "ENSP00000394883.1",
"transcript_support_level": 2,
"aa_start": 137,
"aa_end": null,
"aa_length": 285,
"cds_start": 409,
"cds_end": null,
"cds_length": 858,
"cdna_start": 411,
"cdna_end": null,
"cdna_length": 903,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "c.430C>A",
"hgvs_p": "p.Pro144Thr",
"transcript": "ENST00000442195.5",
"protein_id": "ENSP00000405227.1",
"transcript_support_level": 3,
"aa_start": 144,
"aa_end": null,
"aa_length": 167,
"cds_start": 430,
"cds_end": null,
"cds_length": 504,
"cdna_start": 536,
"cdna_end": null,
"cdna_length": 610,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "c.343C>A",
"hgvs_p": "p.Pro115Thr",
"transcript": "ENST00000496612.5",
"protein_id": "ENSP00000419229.1",
"transcript_support_level": 3,
"aa_start": 115,
"aa_end": null,
"aa_length": 132,
"cds_start": 343,
"cds_end": null,
"cds_length": 399,
"cdna_start": 739,
"cdna_end": null,
"cdna_length": 795,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "n.148C>A",
"hgvs_p": null,
"transcript": "ENST00000460489.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1077,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "n.777C>A",
"hgvs_p": null,
"transcript": "ENST00000476953.6",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 781,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "n.129C>A",
"hgvs_p": null,
"transcript": "ENST00000488605.1",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 572,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "n.156C>A",
"hgvs_p": null,
"transcript": "ENST00000495157.5",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 641,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "n.474C>A",
"hgvs_p": null,
"transcript": "NR_135322.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1234,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "n.1145C>A",
"hgvs_p": null,
"transcript": "NR_135323.3",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2070,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETDB2-PHF11",
"gene_hgnc_id": null,
"hgvs_c": "n.2993C>A",
"hgvs_p": null,
"transcript": "NR_135324.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3918,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"hgvs_c": "n.*24C>A",
"hgvs_p": null,
"transcript": "ENST00000467763.5",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 703,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PHF11",
"gene_hgnc_id": 17024,
"dbsnp": "rs145656056",
"frequency_reference_population": 0.00006602962,
"hom_count_reference_population": 0,
"allele_count_reference_population": 103,
"gnomad_exomes_af": 0.0000660629,
"gnomad_genomes_af": 0.000065722,
"gnomad_exomes_ac": 93,
"gnomad_genomes_ac": 10,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.03558984398841858,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.07,
"revel_prediction": "Benign",
"alphamissense_score": 0.0797,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.42,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.291,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000378319.8",
"gene_symbol": "PHF11",
"hgnc_id": 17024,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.547C>A",
"hgvs_p": "p.Pro183Thr"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_001320727.2",
"gene_symbol": "SETDB2-PHF11",
"hgnc_id": null,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.2029C>A",
"hgvs_p": "p.Pro677Thr"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}